Proteins: Structure, Function, and Bioinformatics

Cover image for Vol. 79 Issue 12

Special Issue: Protein Electrostatics Calculations: Critical Assessment of Progress and Problems

December 2011

Volume 79, Issue 12

Pages 3249–3524

Issue edited by: Jens E. Nielsen, Marilyn R. Gunner

  1. Reviews

    1. Top of page
    2. Reviews
    3. Research Articles
    4. Articles
    5. Research Articles
    6. Articles
    7. Research Articles
    1. Progress in the prediction of pKa values in proteins (pages 3260–3275)

      Emil Alexov, Ernest L. Mehler, Nathan Baker, António M. Baptista, Yong Huang, Francesca Milletti, Jens Erik Nielsen, Damien Farrell, Tommy Carstensen, Mats H. M. Olsson, Jana K. Shen, Jim Warwicker, Sarah Williams and J. Michael Word

      Article first published online: 15 OCT 2011 | DOI: 10.1002/prot.23189

  2. Research Articles

    1. Top of page
    2. Reviews
    3. Research Articles
    4. Articles
    5. Research Articles
    6. Articles
    7. Research Articles
    1. Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics (pages 3276–3286)

      Evan J. Arthur, Joseph D. Yesselman and Charles L. Brooks III

      Article first published online: 15 OCT 2011 | DOI: 10.1002/prot.23195

    2. On the development of protein pKa calculation algorithms (pages 3287–3298)

      Tommy Carstensen, Damien Farrell, Yong Huang, Nathan A. Baker and Jens Erik Nielsen

      Article first published online: 8 JUL 2011 | DOI: 10.1002/prot.23091

  3. Articles

    1. Top of page
    2. Reviews
    3. Research Articles
    4. Articles
    5. Research Articles
    6. Articles
    7. Research Articles
  4. Research Articles

    1. Top of page
    2. Reviews
    3. Research Articles
    4. Articles
    5. Research Articles
    6. Articles
    7. Research Articles
    1. Electrostatic pKa computations in proteins: Role of internal cavities (pages 3320–3332)

      Tim Meyer, Gernot Kieseritzky and Ernst-Walter Knapp

      Article first published online: 8 JUL 2011 | DOI: 10.1002/prot.23092

    2. Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy (pages 3364–3373)

      Jason A. Wallace, Yuhang Wang, Chuanyin Shi, Kevin J. Pastoor, Bao-Linh Nguyen, Kai Xia and Jana K. Shen

      Article first published online: 11 JUL 2011 | DOI: 10.1002/prot.23080

  5. Articles

    1. Top of page
    2. Reviews
    3. Research Articles
    4. Articles
    5. Research Articles
    6. Articles
    7. Research Articles
  6. Research Articles

    1. Top of page
    2. Reviews
    3. Research Articles
    4. Articles
    5. Research Articles
    6. Articles
    7. Research Articles
    1. You have full text access to this OnlineOpen article
      Measuring the successes and deficiencies of constant pH molecular dynamics: A blind prediction study (pages 3381–3388)

      Sarah L. Williams, Patrick G. Blachly and J. Andrew McCammon

      Article first published online: 30 AUG 2011 | DOI: 10.1002/prot.23136

    2. Developing hybrid approaches to predict pKa values of ionizable groups (pages 3389–3399)

      Shawn Witham, Kemper Talley, Lin Wang, Zhe Zhang, Subhra Sarkar, Daquan Gao, Wei Yang and Emil Alexov

      Article first published online: 8 JUL 2011 | DOI: 10.1002/prot.23097

    3. Histidine in continuum electrostatics protonation state calculations (pages 3410–3419)

      Vernon Couch and Alexei Stuchebrukhov

      Article first published online: 30 AUG 2011 | DOI: 10.1002/prot.23114

    4. pH replica-exchange method based on discrete protonation states (pages 3420–3436)

      Satoru G. Itoh, Ana Damjanović and Bernard R. Brooks

      Article first published online: 15 OCT 2011 | DOI: 10.1002/prot.23176

    5. Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase (pages 3448–3468)

      Savvas Polydorides, Najette Amara, Caroline Aubard, Pierre Plateau, Thomas Simonson and Georgios Archontis

      Article first published online: 11 MAY 2011 | DOI: 10.1002/prot.23042

    6. Energetics of charge–charge interactions between residues adjacent in sequence (pages 3494–3499)

      Vakhtang V. Loladze and George I. Makhatadze

      Article first published online: 30 AUG 2011 | DOI: 10.1002/prot.23132

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